The unidentified pilot was pulled from the ocean and was reported to be in good condition aboard a U.S. civilian ship, the 35th Fighter Wing said in a written statement.
"We are thankful for the support from our Japanese friends and other agencies committed to ensuring the safe recovery of our airman," said Col. Al Wimmer, the vice commander of the wing.
The single-seat F-16 had left Misawa Air Force Base on a trans-Pacific flight to somewhere in North America when it ran into trouble about 250 miles of the island of Hokkaido.
The jet was based at Misawa. The cause of the crash was under investigation.